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(-) Description

Title :  INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH IP6.
 
Authors :  B. Gonzalez, J. I. Banos-Sanz, M. Villate, C. A. Brearley, J. Sanz-Aparicio
Date :  31 Mar 10  (Deposition) - 19 May 10  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Ipk, Insp5 2-K, Phytic Acid Synthase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Gonzalez, J. I. Banos-Sanz, M. Villate, C. A. Brearley, J. Sanz-Aparicio
Inositol 1, 3, 4, 5, 6-Pentakisphosphate 2-Kinase Is A Distant Ipk Member With A Singular Inositide Binding Site For Axial 2-Oh Recognition.
Proc. Natl. Acad. Sci. Usa V. 107 9608 2010
PubMed-ID: 20453199  |  Reference-DOI: 10.1073/PNAS.0912979107

(-) Compounds

Molecule 1 - INOSITOL-PENTAKISPHOSPHATE 2-KINASE
    Chains: A, B
    EC Number: 2.7.1.158
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKLSLT
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE, INS(1,3,4,5,6)P5 2-KINASE, INSP5 2-KINASE, ATIPK1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1I6P2Ligand/IonINOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1I6P1Ligand/IonINOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1I6P1Ligand/IonINOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , GLY A:20 , ALA A:21 , ARG A:45 , ARG A:130 , LYS A:168 , LYS A:170 , HIS A:196 , LYS A:200 , ASN A:238 , ASP A:368 , LYS A:411 , ARG A:415 , TYR A:419BINDING SITE FOR RESIDUE I6P A 500
2AC2SOFTWAREHIS A:320 , CYS A:330 , CYS A:333 , HIS A:346BINDING SITE FOR RESIDUE ZN A 700
3AC3SOFTWAREGLY B:19 , GLY B:20 , ALA B:21 , ARG B:45 , ARG B:130 , LYS B:168 , LYS B:170 , LYS B:200 , ASN B:238 , ASP B:368 , LYS B:411 , ARG B:415 , TYR B:419BINDING SITE FOR RESIDUE I6P B 500
4AC4SOFTWAREHIS B:320 , CYS B:330 , CYS B:333 , HIS B:346BINDING SITE FOR RESIDUE ZN B 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XAR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XAR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XAR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XAR)

(-) Exons   (0, 0)

(no "Exon" information available for 2XAR)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:417
 aligned with IPPK_ARATH | Q93YN9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:435
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432     
           IPPK_ARATH     3 MILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKNANGVVSVLTSDEQHLWRENNELISSPNKEVLEQRYVKNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQGISSGGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYNEISEESEYDPLDLFSGSKESVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHSYYDLINQPCPICKEGKPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAE 437
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhh.eeeeee...eeeeee.........eeeeeeeee...----------...hhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhhhhhheee.....eeeeee........--.....eeeee................hhhhhh.hhhhhhhhhhhhh.........hhhhhhh.hhhhhhhhhhhhhhh....eeeee..eeee..........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.........------hhhhhh.hhhhhhhhhhhhhhhhhhhhheeeeeeee...........eeee....eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xar A   3 MILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRND----------SVLTSDEQHLWRENNELISSPNKEVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQG--SGGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPICKE------ELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAE 437
                                    12        22        32        42     |   -      | 62        72        82        92       102       112       122       132       142       152  |  | 162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332  |    342       352       362       372       382       392       402       412       422       432     
                                                                        48         59                                                                                             155  |                                                                                                                                                                              335    342                                                                                               
                                                                                                                                                                                     158                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:424
 aligned with IPPK_ARATH | Q93YN9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:436
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432      
           IPPK_ARATH     3 MILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKNANGVVSVLTSDEQHLWRENNELISSPNKEVLEQRYVKNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQGISSGGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYNEISEESEYDPLDLFSGSKESVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHSYYDLINQPCPICKEGKPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAEN 438
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------Ins_P5_2-kin-2xarB01 B:15-426                                                                                                                                                                                                                                                                                                                                                                                               ------------ Pfam domains (1)
           Pfam domains (2) ------------Ins_P5_2-kin-2xarB02 B:15-426                                                                                                                                                                                                                                                                                                                                                                                               ------------ Pfam domains (2)
         Sec.struct. author ...hhhhhh.eeeeee...eeeeee.........eeeeeeeee........---.....hhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhhhhhhhheee.....eeeeee........---...eeeeee................hhhhhh.hhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhh....eeeee..eeee..........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh............--hhhhhhh.hhhhhhhhhhhhhhhhhhhhheeeeeeee..----.....eeeehhhheeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xar B   3 MILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKN---VVSVLTSDEQHLWRENNELISSPNKEVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQG---GGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPICKEGRP--AELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRN----EPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAEN 438
                                    12        22        32        42        52|   |   62        72        82        92       102       112       122       132       142       152  |   |162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     | 342       352       362       372      |  - |     392       402       412       422       432      
                                                                             53  57                                                                                               155 159                                                                                                                                                                                338  |                                   379  384                                                      
                                                                                                                                                                                                                                                                                                                                                                            341
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2XAR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XAR)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Ins_P5_2-kin] (4)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IPPK_ARATH | Q93YN9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0035299    inositol pentakisphosphate 2-kinase activity    Catalysis of the reaction: 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ATP = 1D-myo-inositol hexakisphosphate + ADP + 2 H(+).
    GO:0032942    inositol tetrakisphosphate 2-kinase activity    Catalysis of the reaction: 1D-myo-inositol tetrakisphosphate + ATP = 1D-myo-inositol pentakisphosphate (containing 2-phosphate) + ADP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0030643    cellular phosphate ion homeostasis    Any process involved in the maintenance of an internal steady state of phosphate ions at the level of a cell.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0048527    lateral root development    The process whose specific outcome is the progression of the lateral root over time, from its formation to the mature structure. A lateral root is one formed from pericycle cells located on the xylem radius of the root, as opposed to the initiation of the main root from the embryo proper.
    GO:0010264    myo-inositol hexakisphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of phytic acid, myo-inositol hexakisphosphate, a regulator of intracellular signaling, a highly abundant animal anti-nutrient and a phosphate and mineral storage compound in plant seeds.
    GO:0055062    phosphate ion homeostasis    Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  2.7.1.158
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IPPK_ARATH | Q93YN9: 2xal 2xam 2xan 2xao 3uds 3udt 3udz 4aqk 4axc 4axd 4axe 4axf 4lv7

(-) Related Entries Specified in the PDB File

2xal LEAD DERIVATIVE OF INOSITOL 1,3,4,5,6- PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH ADP AND IP6.
2xam INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2- KINASE FROM A. THALIANA IN COMPLEX WITH ADP AND IP6.
2xan INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2- KINASE FROM A. THALIANA IN COMPLEX WITH AMP PNP AND IP5
2xao INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2- KINASE FROM A. THALIANA IN COMPLEX WITH IP5